Sampling efficiency of molecular dynamics and Monte Carlo method in protein simulation

Molecular dynamics (MD) and Monte Carlo (MC) method were compared in terms of the sampling efficiency in protein simulations. In the comparison, both methods use torsion angles as the degrees of freedom and the same force fie ld, ECEPP/2. The MC method used here is the force-bias scaled-collective-va riable Monte Carlo (SCV MC) [A. Kidera, Int. J. Quant. Chem. 75 (1999) 207] , which corresponds to a finite step size extension to Brownian dynamics. I t is shown that MD has about 1.5 times larger sampling efficiency. This dif ference is attributed to the inertia force term in MD, which does not exist in MC. (C) 2001 Elsevier Science B.V. All rights reserved.